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3on7

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of a Putative oxygenase (SO_2589) from Shewanella oneidensis at 2.20 A resolution. To be published
    Site JCSG
    PDB Id 3on7 Target Id 398694
    Molecular Characteristics
    Source Shewanella oneidensis mr-1
    Alias Ids TPS29658,NP_718175.1, _0076.002207_, 324904 Molecular Weight 31733.19 Da.
    Residues 279 Isoelectric Point 5.25
    Sequence mkletidyraadsakrfveslretgfgvlsnhpidkelveriytewqaffnseaknefmfnrethdgff pasisetakghtvkdikeyyhvypwgripdslranilayyekantlasellewietyspdeikakfsip lpemianshktllrilhyppmtgdeemgairaaahedinlitvlptanepglqvkakdgswldvpsdfg niiinigdmlqeasdgyfpstshrvinpegtdktksrislplflhphpsvvlserytadsylmerlrelgvl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.20 Rfree 0.2345
    Matthews' coefficent 2.24 Rfactor 0.1847
    Waters 691 Solvent Content 45.00

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3on7
    1. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     
    2. Protein Physics by Advanced Computational Techniques: Conformational Sampling and Folded State Discrimination
    PC Tejada - 2011 - sissa.it
     

    Protein Summary

    Pfam Update: This structure matches to 2OG-FeII_Oxy (PF03171) family. Many structures are already known, so not so interesting to us. However, I do note that we struggle to routinely match the full length of this domain.

     

    Target ID 398694 belongs to the 2-OG-Fe(II) oxygenase (PF03171) Pfam family. This Pfam family is represented by 73 structures in the PDB.

     

    monomer.png

     

    Shown here is a ribbons representation of the monomeric structure of target ID 398694 with the N-terminal end in blue and the C-terminal end in red. The architecture of target ID 398694 is similar to that of proteins belonging to the clavaminate synthease-like Superfamily. Members of this family show a central double-stranded beta-helix SCOP fold.

     

     

     

     

     

     

     

     

    dimer.png

     

     

     

     

    The crystal structure of target ID 398694 suggests that a tetramer is a significant oligomerization state in solution. Shown here is a ribbons representation of a tetramer with the individual monomers in a different color.

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    A DALI search indicates that target ID 398694 shows similarity to the following structures:

     

    PDB ID
    DALI Z-Score
    rmsd overlap (Angstroms)
    length of alignment
    number of residues in PDB hit
    sequence ID (%)
    Description
    Citation
    1IPS_A 24.4 2.6 248 328 23 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX) [Ref]
    1OC1_A 24.4 2.7 248 329 23 ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL-AMINOBUTYRATE-FE COMPLEX [Ref]
    1ODN_A 24.4 2.7 248 321 23 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN-EXPOSED PRODUCT FROM ANAEROBIC AC-VINYLGLYCINE FE COMPLEX) [Ref]
    2BJS_A 24.4 2.5 245 320 23

    ISOPENICILLIN N SYNTHASE C-TERMINAL TRUNCATION MUTANT

     
     
    2BRT_A 24.3 2.8 251 348 22 ANTHOCYANIDIN SYNTHASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH NARINGENIN [Ref]
    2JB4_A 24.3 2.5 245 329 23 ISOPENICILLIN N SYNTHASE WITH A 2-THIABICYCLOHEPTAN-6-ONE PRODUCT ANALOGUE [Ref]
    1GP6_A 24.2 2.8 251 349 22 ANTHOCYANIDIN SYNTHASE FROM ARABIDOPSIS THALIANA COMPLEXED WITH TRANS-DIHYDROQUERCETIN (WITH 30 MIN EXPOSURE TO O2) [Ref]

     

     

     Two related JCSG structures have been determined that belong to the 2OG-Fe(II) oxygenase Pfam family. These two JCSG strucuctures are target ID 398027 and and PDB ID 3dkq.

     

    MI15887SP_MI15887P_overlap.png

    Shown here is an overlap between target ID 398694 (green) and target ID 398027 (yellow). The two targets share 32% sequence identity with an rmsd overlap of 2.0 Angstroms over 253 residues. A significant structural difference between the two proteins is that target ID 398027 (yellow) contains an insertion loop with a short helix between residues 100-120

     

     

    Ligand Summary

    Reviews

    References

     

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